Fix bug: boolean

defaults

@@ -13,12 +13,12 @@
     "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
     "database": "oss://pgx-reference-data/annovar_hg38/",
     "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
-    "set_pon": true,
+    "set_pon": "true",
     "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
     "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
     "disk_size": "200",
     "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "set_annovar": true,
-    "set_vcf2maf": true,
-    "germline": false
+    "set_annovar": "true",
+    "set_vcf2maf": "true",
+    "germline": "false"
 }

tasks/TNscope.wdl

@@ -19,12 +19,12 @@ task TNscope {
 	String dbsnp
 	String disk_size
 
-	Boolean set_pon
+	String set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
 	File? pon_vcf
 	
-	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
+	String pon_command = if (set_pon == "true") then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
 	Boolean TN = if defined(corealigner_bam) then true else false
 	
 	command <<<

tasks/TNseq.wdl

@@ -17,12 +17,12 @@ task TNseq {
 	String dbsnp
 	String disk_size
 
-	Boolean set_pon
+	String set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
 	File? pon_vcf
 	
-	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
+	String pon_command = if (set_pon == "true") then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
 	Boolean TN = if defined(corealigner_bam) then true else false
 
 	command <<<

tasks/bcftools.wdl

@@ -4,14 +4,14 @@ task bcftools {
 	String docker
 	String cluster_config
 	String disk_size
-	Boolean set_pon
+	String set_pon
 
 
 	command <<<
 		set -o pipefail
 		set -e
 		
-		if ${set_pon} ; then
+		if [ ${set_pon} == "true" ] ; then
 			mkdir -p /cromwell_root/tmp/bcftools/
 			for i in ${sep=" " pon_vcf}
 			do

workflow.wdl

@@ -38,15 +38,15 @@ workflow {{ project_name }} {
 	String disk_size
 	String cluster_config
 
-	Boolean set_pon
+	String set_pon
 	File? pon_vcf
 	File? cosmic_dir
 	String? cosmic_vcf
 
-	Boolean set_annovar
+	String set_annovar
 	File? database
-	Boolean set_vcf2maf
-	Boolean germline
+	String set_vcf2maf
+	String germline
 
 
 	call mapping.mapping as mapping {
@@ -141,7 +141,7 @@ workflow {{ project_name }} {
 		cluster_config=cluster_config
 	}
 
-	if (set_pon && type == "normal") {
+	if (set_pon == "true" && type == "normal") {
 		call PON.PON as PON {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
@@ -161,7 +161,7 @@ workflow {{ project_name }} {
 		}
 	}
 
-	if (germline) {
+	if (germline == "true") {
 		call Haplotyper.Haplotyper as Haplotyper {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
@@ -252,7 +252,7 @@ workflow {{ project_name }} {
 		}
 	}
 
-	if (set_annovar && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
+	if (set_annovar == "true" && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
 		call annovar.annovar as annovar {
 			input:
 			docker=annovar_docker,
@@ -264,7 +264,7 @@ workflow {{ project_name }} {
 			disk_size=disk_size
 		}
 
-		if (set_vcf2maf){
+		if (set_vcf2maf == "true"){
 			call vcf2maf.vcf2maf as vcf2maf {
 				input:
 				docker=maftools_docker,